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Plot traces from list of chromatograms

Source: R/plot_chroms.R
plot_chroms.Rd

Visualizes absorbance traces from a list of one- or multi-wavelength chromatograms using base R, ggplot2, or plotly graphics. For multi-wavelength chromatograms, one or more wavelengths can be selected using lambdas. Traces are thinned to time_resolution before plotting. Each chromatogram specified by idx is plotted as a separate trace in its own color.

Usage

plot_chroms(
  x,
  lambdas = NULL,
  idx,
  time_resolution = 0.01,
  time_unit = NULL,
  xlim = NULL,
  ylim = NULL,
  xlab = "",
  ylab = "Absorbance",
  engine = c("base", "ggplot", "plotly"),
  linewidth = 1,
  show_legend = FALSE,
  legend_position = "topright",
  title = "",
  what = NULL,
  ...
)

Arguments

x

A list of chromatograms in matrix format (timepoints × wavelengths) or a peak_table containing a pointer to a list of chromatograms accessible in the current environment.

lambdas

A character or numeric vector specifying the wavelengths to plot. Required for multi-wavelength chromatograms and optional for one-dimensional ones, where a supplied wavelength must match the column name.

idx

A vector representing the names or numerical indices of the chromatograms to plot. Defaults to all chromatograms.

time_resolution

Desired temporal resolution for plotting (in minutes). Chromatograms are thinned to approximately this interval prior to plotting, which speeds up rendering of large datasets. Defaults to 0.01.

time_unit

Time units of the provided chromatograms: either min, s, or ms. If possible, units will be detected automatically from chromatogram metadata. If time_unit attribute is not present and no argument is provided, the time units will default to minutes.

xlim

Range of x axis values. Unless ylim is given, the y axis is then fitted to the traces within this range.

ylim

Range of y axis values.

xlab

X label.

ylab

Y label. Defaults to "Absorbance".

engine

Plotting backend to use. One of "base", "ggplot", or "plotly".

linewidth

Line width. Defaults to 1.

show_legend

Logical. Whether to display a legend. Defaults to FALSE.

legend_position

Position of legend. Defaults to "topright". For engine = "base", a top or bottom keyword spreads the entries over columns and, unless ylim is given, widens the y-range so the legend clears the traces. For engine = "ggplot", any value accepted by the legend.position argument of ggplot2::theme(); the default leaves ggplot2's own placement.

title

Title for plot.

what

Which element to plot when each chromatogram in x is itself a list, as returned by chromConverter::read_chroms() with several what values. A single name (e.g. "dad"), or a vector of names for a nested element (e.g. c("instrument", "PMP1, Pressure")). A nested element can also be written as one string split at the first colon, as in "instrument:PMP1, Pressure", unless that string is itself an element name. Defaults to "dad" for such lists; ignored when x is a list of matrices.

...

Additional arguments to matplot (engine = "base"), ggplot2::geom_line() (engine = "ggplot"), or the line list of plotly::plot_ly() (engine = "plotly").

Value

A plotly or ggplot object when engine = "plotly" or engine = "ggplot", respectively. No value is returned when engine = "base".

Side effects

If engine == "base", the plot is rendered to the active graphics device.

See also

Other visualization functions: boxplot.peak_table(), mirror_plot(), plot.chrom_list(), plot.matched_peak_list(), plot.peak_list(), plot.peak_table(), plot_all_spectra(), plot_chrom_contour(), plot_chroms_heatmap(), plot_spectrum(), scan_chrom()

Author

Ethan Bass

Examples

data(Sa_warp)
plot_chroms(Sa_warp, lambdas = 210)